Foundations#
Welcome to the Foundations of MolSysMT. This section introduces the core principles, architectural invariants, and high-performance design that enable MolSysMT to operate seamlessly across different molecular structures, file formats, and computational tools.
Rather than treating molecular systems as rigid data structures bound to a specific software package, MolSysMT builds a form-agnostic bridge. Here you will learn how systems are defined, how physical units and quantities are safely enforced, how selection syntaxes are interpreted, and how native representations ensure speed and interoperability across the structural biology ecosystem. Explore the 8 pillars below to master the underlying framework.
Sections#
Mission, installation, first steps, toolbox overview, and demo systems.
Definition, normalization, items and forms, forms, elements, and attributes.
Native representations, topologies, H5MSM storage, and ViewerJSON.
Selection language, atom queries, and syntactic rules.
Memory management, big data trajectories, and parallelization.
Quantities, physical units, precision policies, and SMonitor.
Compatibility matrix across forms, libraries, and engines.
3D Viewers, MolSysViewer, and third-party integrations.